Interpretive Summary: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an economical and sustainable protein replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth of trout fed plant-based diets in rainbow trout. Evaluating global gene expression in fish on both plant and fishmeal diets we were able to identify activation of metabolic interactions specific to dietary utilization and determine that fish fed a plant-based diet up-regulate areas of their immune system.

Technical Abstract:
Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an economical and sustainable protein replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth of trout fed plant-based diets in rainbow trout. Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation.
Results: Microarray analysis of liver samples was conducted using two families of rainbow trout that differed in their growth responses when compared between individuals fed a fish meal or plant protein base diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions.
Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant-based diet up-regulated the expression of genes involved in immunoregulatory processes.